LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# SRD diffusion demo - dimer particles

units           lj
atom_style      sphere
atom_modify     map array first big
dimension       2

# read in clusters of rigid bodies

fix             molprop all property/atom mol ghost yes
read_data       data.dimer fix molprop NULL Molecules
Reading data file ...
  orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
  2 by 2 by 1 MPI processor grid
  reading atoms ...
  200 atoms
  read_data CPU = 0.001 seconds

set             type 1 mass 1.0
Setting atom values ...
  200 settings made for mass
group           big type 1
200 atoms in group big
velocity        big create 1.44 87287 loop geom

# equilibrate big particles

pair_style      soft 1.12
pair_coeff      1 1 0.0
pair_coeff      2 2 0.0 0.0
pair_coeff      1 2 0.0 0.0

variable        prefactor equal ramp(0,60)
fix             soft all adapt 1 pair soft a * * v_prefactor

fix             1 big rigid molecule
  100 rigid bodies with 200 atoms
fix             2 all enforce2d

#dump           1 all atom 10 dump.dimer.equil

thermo          100
run             1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.42
  ghost atom cutoff = 1.42
  binsize = 0.71, bins = 27 27 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair soft, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.553 | 5.553 | 5.553 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   3.4028231      0              0              0.83369167    -0.55065517   
       100   9.5167872      2.392105       0              4.7237178      2.8319556    
       200   13.564465      3.0352634      0              6.3585572      3.6388732    
       300   13.133051      4.3835112      0              7.6011086      4.060051     
       400   14.576837      5.5141059      0              9.0854309      4.422762     
       500   15.227825      6.6472106      0              10.378028      4.8598912    
       600   16.93219       7.454865       0              11.603251      5.2908894    
       700   16.573769      8.7323442      0              12.792918      5.3544684    
       800   17.482599      9.7221047      0              14.005341      5.6200973    
       900   18.548144      10.739353      0              15.283649      4.7817995    
      1000   18.068079      12.058417      0              16.485096      6.5773093    
Loop time of 0.0424792 on 4 procs for 1000 steps with 200 atoms

Performance: 10169676.521 tau/day, 23540.918 timesteps/s, 4.708 Matom-step/s
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0022758  | 0.0023448  | 0.002442   |   0.1 |  5.52
Neigh   | 0.0011082  | 0.0011236  | 0.0011582  |   0.1 |  2.64
Comm    | 0.0099484  | 0.010092   | 0.010247   |   0.1 | 23.76
Output  | 9.551e-05  | 0.00010604 | 0.00013381 |   0.0 |  0.25
Modify  | 0.026025   | 0.026222   | 0.026405   |   0.1 | 61.73
Other   |            | 0.00259    |            |       |  6.10

Nlocal:             50 ave          55 max          47 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost:          33.75 ave          38 max          32 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Neighs:          68.75 ave          77 max          64 min
Histogram: 2 0 0 1 0 0 0 0 0 1

Total # of neighbors = 275
Ave neighs/atom = 1.375
Neighbor list builds = 193
Dangerous builds = 0

#undump         1
unfix           soft
unfix           1
unfix           2

# add small particles as hi density lattice

region          plane block INF INF INF INF -0.001 0.001 units box
lattice         sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms    2 region plane
Created 29929 atoms
  using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
  create_atoms CPU = 0.002 seconds

set             type 2 mass 0.1
Setting atom values ...
  29929 settings made for mass
group           small type 2
29929 atoms in group small
velocity        small create 1.0 593849 loop geom

# delete overlaps
# must set 1-2 cutoff to non-zero value

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0
pair_coeff      2 2 0.0 1.0 0.0
pair_coeff      1 2 0.0 1.0 0.5

delete_atoms    overlap 0.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 14 14 1
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command delete_atoms, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/2d
      bin: standard
  (2) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 12776 atoms, new total = 17353

# SRD run

reset_timestep  0

neighbor        0.3 multi
neigh_modify    delay 0 every 1 check yes

comm_modify     mode multi group big vel yes
neigh_modify    include big

# no pairwise interactions with small particles

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0
pair_coeff      2 2 0.0 1.0 0.0
pair_coeff      1 2 0.0 1.0 0.0

# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles

timestep        0.001

fix             1 big rigid molecule
  100 rigid bodies with 200 atoms
fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 collision slip inside ignore overlap yes
fix             3 all enforce2d

# diagnostics

compute         tbig big temp/sphere
variable        pebig equal pe*atoms/count(big)
variable        ebig equal etotal*atoms/count(big)
thermo_style    custom step temp f_2[8] etotal v_pebig v_ebig press                 f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]                 f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]

thermo_modify   temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo          1000

#dump           1 all atom 1000 dump.dimer

#dump           1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify    1 pad 6 adiam 1 1 adiam 2 0.2

run             10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2

@Article{Intveld08,
 author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
 title =   {Accurate and Efficient Methods for Modeling Colloidal
            Mixtures in an Explicit Solvent using Molecular Dynamics},
 journal = {Comput.\ Phys.\ Commut.},
 year =    2008,
 volume =  179,
 pages =   {320--329}
}

@article{Shire2020,
 author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
 title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
          Detection Applied to Investigate the Quasi-Static Limit},
 journal = {Computational Particle Mechanics},
 year = {2020}
@article{Monti2022,
 author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
           and Lechman, Jeremy B.},
 title = {Large-scale frictionless jamming with power-law particle 
          size distributions},
 journal = {Phys. Rev. E},
 volume = {106}
 issue = {3}
 year = {2022}
}

- fix srd command: doi:10.1063/1.3419070

@Article{Petersen10,
 author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
 G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
 title =   {Mesoscale Hydrodynamics via Stochastic Rotation
    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
 journal = {J.~Chem.\ Phys.},
 year =    2010,
 volume =  132,
 pages =   174106
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
  SRD/big particles = 17153 200
  big particle diameter max/min = 1 1
  SRD temperature & lamda = 1 0.063245553
  SRD max distance & max velocity = 0.25298221 12.649111
  SRD grid counts: 75 75 1
  SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
  SRD per actual grid cell = 5.544404
  SRD viscosity = 0.23553122
  big/SRD mass density ratio = 0.14250828
  # of rescaled SRD velocities = 0
  ave/max small velocity = 4.191188 7.6900178
  ave/max big velocity = 2.6813242 7.1846103
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 18.683304, bins = 1 1 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/multi/atomonly/newton
      stencil: half/multi/2d
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 13.2 | 13.21 | 13.22 Mbytes
   Step          Temp          f_2[8]         TotEng        v_pebig         v_ebig         Press          f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]         f_2[6]         f_2[7]         f_2[8]         f_2[9]        f_2[10]        f_2[11]        f_2[12]    
         0   6.8392143      0              0.297476       20.71529       25.810505      4.0555746      0              0              0              0              0              0              0              0              0              0              0              0            
      1000   1.1648085      3389           0.24643931     20.514525      21.382307      5.5927686      13390          59             59             0              1015           28224          5625           3389           1.1513276      0              111            0            
      2000   1.1870311      3385           0.24701637     20.548037      21.432375      5.9269821      13271          57             57             2              1878           28224          5625           3385           1.1619099      0              111            0            
      3000   1.1362839      3365           0.24577276     20.477942      21.324474      5.1621045      13244          59             60             1              2778           28224          5625           3365           1.1807679      0              111            0            
      4000   1.3023748      3390           0.24679509     20.442907      21.413176      5.6127077      13413          65             65             1              3705           28224          5625           3390           1.1726946      0              111            0            
      5000   1.195496       3387           0.2458055      20.43667       21.327314      6.1843476      13248          51             51             1              4638           28224          5625           3387           1.1730279      0              111            0            
      6000   1.2389419      3387           0.24546635     20.374876      21.297888      5.5909826      13184          54             54             1              5494           28224          5625           3387           1.1859134      0              111            0            
      7000   1.2068912      3378           0.24564722     20.414447      21.313581      8.5604547      13188          57             57             1              6428           28224          5625           3378           1.1499181      0              111            0            
      8000   1.1014154      3374           0.24514746     20.449665      21.270219      7.3483529      13179          63             63             0              7591           28224          5625           3374           1.1769322      0              121            0            
      9000   1.356464       3388           0.24749513     20.463349      21.473915      7.6809833      13138          50             50             2              8485           28224          5625           3388           1.1448659      0              121            0            
     10000   1.1632951      3402           0.24560819     20.44354       21.310195      9.5738599      13323          64             67             0              9304           28224          5625           3402           1.1550136      0              121            0            
Loop time of 2.47185 on 4 procs for 10000 steps with 17353 atoms

Performance: 349536.432 tau/day, 4045.561 timesteps/s, 70.203 Matom-step/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.037524   | 0.039903   | 0.042215   |   1.1 |  1.61
Neigh   | 0.01053    | 0.010805   | 0.011068   |   0.2 |  0.44
Comm    | 0.14536    | 0.14822    | 0.15102    |   0.6 |  6.00
Output  | 0.00051847 | 0.00054674 | 0.0006272  |   0.0 |  0.02
Modify  | 2.2276     | 2.2334     | 2.2381     |   0.3 | 90.35
Other   |            | 0.03895    |            |       |  1.58

Nlocal:        4338.25 ave        4488 max        4277 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Nghost:          76.75 ave          85 max          69 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs:         331.25 ave         355 max         306 min
Histogram: 1 0 0 1 0 0 1 0 0 1

Total # of neighbors = 1325
Ave neighs/atom = 0.076355673
Neighbor list builds = 507
Dangerous builds = 0
Total wall time: 0:00:02
